MolNFT v1 · #27509 · protein
Crystal structure of transhydrogenase [(domain I)2:DOMAIN III] heterotrimer complex
1XLT · NAD(P) transhydrogenase subunit alpha part 1: “Crystal structure of transhydrogenase [(domain I)2:DOMAIN III] heterotrimer complex”. X-ray diffraction, 5 ligands (NAD, NDP, GLC), 20 pockets (best druggability 0.82). MolNFT v1 #27509…
- PDB
- 1XLT
- Type
- protein
- Length
- 2,700 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD(P) transhydrogenase subunit alpha part 1; NAD(P) transhydrogenase subunit beta
- EC
- 1.6.1.2
- UniProt
- Q60164, Q59765
- Ligands
- NAD, NDP, GLC, FRU, NA
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 8 distinct chains · 34% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAD(P) transhydrogenase subunit alpha part 1 (EC 1.6.1.2) | protein | 363 | 34% helix, 19% strand | Q60164 |
| B | NAD(P) transhydrogenase subunit alpha part 1 (EC 1.6.1.2) | protein | 359 | 36% helix, 18% strand | Q60164 |
| C | NAD(P) transhydrogenase subunit beta (EC 1.6.1.2) | protein | 174 | 40% helix, 17% strand | Q59765 |
| D | NAD(P) transhydrogenase subunit alpha part 1 (EC 1.6.1.2) | protein | 378 | 30% helix, 15% strand | Q60164 |
| E | NAD(P) transhydrogenase subunit alpha part 1 (EC 1.6.1.2) | protein | 359 | 33% helix, 18% strand | Q60164 |
| F, I | NAD(P) transhydrogenase subunit beta (EC 1.6.1.2) | protein | 173 | 34% helix, 17% strand | Q59765 |
| G | NAD(P) transhydrogenase subunit alpha part 1 (EC 1.6.1.2) | protein | 364 | 35% helix, 20% strand | Q60164 |
| H | NAD(P) transhydrogenase subunit alpha part 1 (EC 1.6.1.2) | protein | 357 | 31% helix, 20% strand | Q60164 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 5 copies · chains A, B, C, D, G, H, I
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 3 copies · chains B, C, E, F, H, I
- GLC · alpha-D-glucopyranose · sugar · 6 copies · chains A, B, D, E, G, H
- FRU · beta-D-fructofuranose · sugar · 6 copies · chains A, B, D, E, G, H
- NA · Sodium ion · metal · 3 copies · chains A, B, D, E, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 990 | 0.82 | 0.83 | 110 | NAD, NDP |
| 2 | 683 | 0.79 | 0.83 | 90 | empty |
| 3 | 498 | 0.78 | 0.85 | 50 | NAD |
| 4 | 957 | 0.76 | 0.79 | 70 | empty |
| 5 | 1142 | 0.76 | 0.78 | 107 | NDP |
Interfaces
15 interfaces between chains.
- D–E · 1790 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1724 Ų buried · 23 hydrogen bonds · protein-protein
- G–H · 1724 Ų buried · 18 hydrogen bonds · protein-protein
- H–I · 805 Ų buried · 8 hydrogen bonds · protein-protein
- E–F · 741 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 1XLT · Crystal structure of Transhydrogenase [(domain I)2:domain III] heterotrimer complex · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q60164
- Every structure of UniProt Q59765
- Elsewhere: RCSB PDB 1XLT · PDBe 1XLT · UniProt Q60164 · UniProt Q59765
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